Keep the type pango_lineage snakecase as this is recognized by LAPIS …

…as a type.
loculus-project · Aug 22, 2024 · 4eba0dd · 4eba0dd
1 parent 997bff1
commit 4eba0dd
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Showing 13 changed files with 14 additions and 14 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/config/Config.kt b/backend/src/main/kotlin/org/loculus/backend/config/Config.kt
@@ -43,7 +43,7 @@ enum class MetadataType {
     @JsonProperty("date")
     DATE,
 
-    @JsonProperty("pangoLineage")
+    @JsonProperty("pango_lineage")
     PANGO_LINEAGE,
 
     @JsonProperty("boolean")

diff --git a/...src/main/kotlin/org/loculus/backend/service/submission/ProcessedSequenceEntryValidator.kt b/...src/main/kotlin/org/loculus/backend/service/submission/ProcessedSequenceEntryValidator.kt
@@ -126,7 +126,7 @@ private fun validateType(fieldValue: JsonNode, metadata: BaseMetadata) {
         MetadataType.PANGO_LINEAGE -> {
             if (!isValidPangoLineage(fieldValue.asText())) {
                 throw ProcessingValidationException(
-                    "Expected type 'pangoLineage' for field '${metadata.name}', " +
+                    "Expected type 'pango_lineage' for field '${metadata.name}', " +
                         "found value '$fieldValue'. " +
                         "A pango lineage must be of the form $PANGO_LINEAGE_REGEX_PATTERN, e.g. 'XBB' or 'BA.1.5'.",
                 )

diff --git a/.../test/kotlin/org/loculus/backend/controller/submission/SubmitProcessedDataEndpointTest.kt b/.../test/kotlin/org/loculus/backend/controller/submission/SubmitProcessedDataEndpointTest.kt
@@ -487,7 +487,7 @@ class SubmitProcessedDataEndpointTest(
                     accession = "DoesNotMatter",
                 ),
                 expectedErrorMessage =
-                "Expected type 'pangoLineage' for field 'pangoLineage', found value '\"A.5.invalid\"'. " +
+                "Expected type 'pango_lineage' for field 'pangoLineage', found value '\"A.5.invalid\"'. " +
                     "A pango lineage must be of the form [a-zA-Z]{1,3}(\\.\\d{1,3}){0,3}, e.g. 'XBB' or 'BA.1.5'.",
             ),
             InvalidDataScenario(

diff --git a/backend/src/test/resources/backend_config.json b/backend/src/test/resources/backend_config.json
@@ -65,7 +65,7 @@
                     },
                     {
                         "name": "pangoLineage",
-                        "type": "pangoLineage",
+                        "type": "pango_lineage",
                         "autocomplete": true
                     },
                     {
@@ -165,7 +165,7 @@
                     },
                     {
                         "name": "pangoLineage",
-                        "type": "pangoLineage",
+                        "type": "pango_lineage",
                         "autocomplete": true
                     },
                     {

diff --git a/backend/src/test/resources/backend_config_single_segment.json b/backend/src/test/resources/backend_config_single_segment.json
@@ -65,7 +65,7 @@
                     },
                     {
                         "name": "pangoLineage",
-                        "type": "pangoLineage",
+                        "type": "pango_lineage",
                         "autocomplete": true
                     },
                     {

diff --git a/docs/src/content/docs/for-administrators/setup-with-kubernetes.md b/docs/src/content/docs/for-administrators/setup-with-kubernetes.md
@@ -98,7 +98,7 @@ organisms:
                   type: string
                   autocomplete: true
                 - name: pangoLineage
-                  type: pangoLineage
+                  type: pango_lineage
                   autocomplete: true
                   required: true
                 - name: insdcAccessionFull

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1329,7 +1329,7 @@ defaultOrganisms:
           header: "Collection Details"
         - name: pangoLineage
           initiallyVisible: true
-          type: pangoLineage
+          type: pango_lineage
           autocomplete: true
           required: true
       website:

diff --git a/preprocessing/specification.md b/preprocessing/specification.md
@@ -117,7 +117,7 @@ The `metadata` field should contain a flat object consisting of the fields speci
 - `int` (integer)
 - `float`
 - `date` (supplied as a string with complete ISO-8601 date, e.g., "2023-08-30")
-- `pangoLineage` (supplied as a string with a properly formatted SARS-CoV-2 Pango lineage, e.g., "B.1.1.7")
+- `pango_lineage` (supplied as a string with a properly formatted SARS-CoV-2 Pango lineage, e.g., "B.1.1.7")
 - `authors` (comma separated list of authors, treated as a string in the current prepro pipeline)
 
 #### Sequences

diff --git a/website/src/components/SearchPage/SearchForm.spec.tsx b/website/src/components/SearchPage/SearchForm.spec.tsx
@@ -29,7 +29,7 @@ const defaultSearchFormFilters: MetadataFilter[] = [
     },
     {
         name: 'field3',
-        type: 'pangoLineage',
+        type: 'pango_lineage',
         label: 'Field 3',
         autocomplete: true,
         initiallyVisible: true,

diff --git a/website/src/components/SearchPage/SearchFullUI.spec.tsx b/website/src/components/SearchPage/SearchFullUI.spec.tsx
@@ -51,7 +51,7 @@ const defaultSearchFormFilters: MetadataFilter[] = [
     },
     {
         name: 'field3',
-        type: 'pangoLineage',
+        type: 'pango_lineage',
         label: 'Field 3',
         autocomplete: true,
         initiallyVisible: true,

diff --git a/website/src/components/SearchPage/fields/FieldProps.tsx b/website/src/components/SearchPage/fields/FieldProps.tsx
@@ -10,5 +10,5 @@ export type FieldProps = {
     onFocus?: FocusEventHandler<HTMLInputElement | HTMLTextAreaElement>;
     onBlur?: FocusEventHandler<HTMLInputElement | HTMLTextAreaElement>;
     fieldValue: string;
-    type?: 'string' | 'boolean' | 'float' | 'int' | 'pangoLineage' | 'authors';
+    type?: 'string' | 'boolean' | 'float' | 'int' | 'pango_lineage' | 'authors';
 };
diff --git a/website/src/components/SearchPage/fields/NormalTextField.tsx b/website/src/components/SearchPage/fields/NormalTextField.tsx
@@ -10,7 +10,7 @@ export type NormalFieldProps = {
     onFocus?: FocusEventHandler<HTMLInputElement | HTMLTextAreaElement>;
     onBlur?: FocusEventHandler<HTMLInputElement | HTMLTextAreaElement>;
     fieldValue: string | number;
-    type?: 'string' | 'boolean' | 'float' | 'int' | 'pangoLineage' | 'authors';
+    type?: 'string' | 'boolean' | 'float' | 'int' | 'pango_lineage' | 'authors';
 };
 
 export const NormalTextField = forwardRef<HTMLInputElement, NormalFieldProps>((props, ref) => {

diff --git a/website/src/types/config.ts b/website/src/types/config.ts
@@ -9,7 +9,7 @@ const metadataPossibleTypes = z.enum([
     'date',
     'int',
     'float',
-    'pangoLineage',
+    'pango_lineage',
     'timestamp',
     'boolean',
     'authors',